Collecting a quality sample for the diagnosis of respiratory diseases presents multiple challenges. The challenges are nuanced between the different disease states but common themes emerge. As an example tuberculosis, influenza and pneumonia are three diseases that each represent particular diagnosis challenges.
Active Tuberculosis (TB) causes approximately 2 million annual deaths, making it the second leading cause of death from infectious diseases worldwide. An estimated 9.3 million people worldwide develop TB every year, of which ˜4.4 million are undiagnosed. TB also poses a significant bioterrorism threat. M. tuberculosis is classified as a NIAID Category C Priority Pathogen and is transmitted primarily through airborne droplets (as few as 2 droplets can cause TB infection). Multiple-drug resistant strains further complicate TB diagnosis and treatment, boosting its threat as a bioterrorism agent. When diagnosed properly TB can be treated. Currently, sputum expectorate is the most common sampling method used for TB diagnosis. Diagnostics that rely on sputum samples suffer from disadvantages associated with sputum collection. Sputum is difficult to collect from some patients (children and elderly), and is unattainable from expectoration deficient patients (˜20% of patients). In these cases, procedures such as sputum induction and gastric aspiration are required; all of which are difficult to administer and risky as they expose healthcare providers to contagious specimens. In other cases, bronchoscopy with bronchoalveolar lavage (BAL) is performed. This procedure is costly, requires a physician, and can cause complications associated with conscious sedation. In the case of a bioterrorist attack, these methods can become prohibitive. When sputum samples are attainable, contamination by oropharyngeal flora, saliva, mucus, and cell debris negatively affects the sensitivity and specificity of diagnostics. Even uncontaminated and undiluted sputum can inherently have low concentrations of M. tuberculosis in patients infected with TB.
Pneumonia is the leading cause of death among infectious diseases in the United States where ˜1.1M people are hospitalized and ˜50,000 die each year. Pneumonia is an infection of the lower respiratory tract (LRT) and is typically caused by viruses and/or bacteria. A major challenge in diagnosing pneumonia is obtaining a quality sample namely because etiologic agents of pneumonia often colonize the upper respiratory tract (URT) of healthy subjects without causing LRT infection. If a diagnostic sample contains URT contaminants, the sample is discarded (low diagnostic yield) or a false etiologic agent may be identified (low specificity). Sputum or bronchoalveolar lavage (BAL) are the most common samples used to identify the etiologic agent of pneumonia. However, both samples suffer significant limitations. Sputum cannot be produced by all patients, particularly in children under the age of 5. Even with the help of induction, sputum is unobtainable in an estimated 40% of pneumonia patients. When collected, sputum samples suffer from contamination of the URT flora, and up to 50% of the samples are discarded. Although BAL provides a higher quality sample for diagnostic analysis, it is invasive, requires sedation, and is therefore only recommended in high-risk patients. As a result, community-acquired pneumonia (CAP) is treated using a broad-spectrum antibiotic regimen in the absence of a diagnostic sample. Since the epidemiology of hospital-acquired pneumonia (HAP) is vastly different than CAP, HAP cannot be treated with the same empirical antibiotic regimen; rather, the identification of an etiology prior to treatment is necessary. In HAP, a BAL is the recommended sample for diagnosis. To obtain an uncompromised sample at minimal risk to patients and encourage antimicrobial stewardship in clinical practice, new methods of non-invasive lower tract sample collection are needed. Better sample collection would serve to improve the <10% yield in the diagnosis of an etiologic agent in CAP and replace invasive procedures in HAP.
Seasonal influenza is a threat to global public health causing 3-5M cases of severe illness and 250,000 deaths each year. Pandemic influenza arises when a new strain, for which little prior immunity exists, begins circulating in the human population. Most recently, the 2009 A(H1N1) swine flu pandemic caused an additional 280,000 deaths. Alarmingly, certain influenza strains, such as the A(H1N1) swine flu and the A(H5N1) avian flu, have an increased propensity to infect the lower respiratory tract and cause severe illness. Influenza diagnosis is typically performed on samples collected from the throat and nasal cavities of the upper respiratory tract, using nasopharyngeal (NP) swabs. However, only invasive procedures can collect samples for the proper diagnosis of lower respiratory tract influenza. In particular, during the recent A(H1N1) pandemic, many influenza cases were diagnosed as negative from NP swab samples but were positive from lower respiratory tract samples. These findings highlight the need to analyze lower respiratory tract samples from patients with severe influenza-like illness. Administration of antiviral therapies can be applied more appropriately, thereby improving patient treatment. Finally, influenza surveillance data collected exclusively from upper respiratory tract samples may miss emerging strains that preferentially target the lower respiratory tract. Current methods of obtaining samples from the lower respiratory tract, such as transtracheal aspiration, bronchoalveolar lavage, and lung biopsy are highly invasive.
Other disease states can also benefit from improvements in sample collection methodologies. These can include but are not limited to Non-tuberculosis mycobacterial infection and respiratory syncytial virus. However, the challenges represented by just these three diseases demonstrate that the field of diagnostics would benefit improved sample collection methodologies.